👤 Gul NS

One of the major challenges in precision oncology is the identification of pathogenic, actionable variants and the selection of personalized treatments. We present Onkopus, a variant interpretation framework based on a modular architecture, for interpreting and prioritizing genetic alterations in cancer patients. A multitude of tools and databases are integrated into Onkopus to provide a comprehensive overview about the consequences of a variant, each with its own semantic, including pathogenicity predictions, allele frequency, biochemical and protein features, and therapeutic options. We present the characteristics of variants and personalized therapies in a clear and concise form, supported by interactive plots. To support the interpretation of variants of unknown significance (VUS), we present a protein analysis based on protein structures, which allows variants to be analyzed within the context of the entire protein, thereby serving as a starting point for understanding the underlying causes of variant pathogenicity. Onkopus has the potential to significantly enhance variant interpretation and the selection of actionable variants for identifying new targets, drug screens, drug testing using organoids, or personalized treatments in molecular tumor boards. We provide a free public instance of Onkopus at https://mtb.bioinf.med.uni-goettingen.de/onkopus. Show less

The photo-induced CO-releasing properties of the dark-stable complex [RuCl₂(CO)₂L] (L = 2-(pyridin-2-yl)quinoxaline) were investigated under 468 nm light exposure in the presence and absence of biomolecules such as histidine, calf thymus DNA and hen egg white lysozyme. The CO release kinetics were consistent regardless of the presence of these biomolecules, suggesting that they did not influence the CO release mechanism. The quinoxaline ligand demonstrated exceptional cytotoxicity against human acute monocytic leukemia cells (THP-1), with evidence of potential DNA damage ascertained by comet assay, while it remained non-toxic to normal kidney epithelial cells derived from African green monkey (Vero) cell lines. In contrast, upon light activation, the Ru(II) complex showed no toxicity against THP-1 cells but was detrimental to Vero cells. In human colorectal carcinoma (HCT-116) cells, the ligand and the Ru(II) complex produced ROS under light and dark conditions. However, HCT-116 cells retained their ability to consume oxygen and produce ATP following CO treatment, suggesting that the ROS levels were insufficient to cause significant cellular damage. Morphological features of apoptosis, including apoptotic bodies, chromatin condensation, cell shrinkage, and membrane leakage, were observed in the presence of both the ligand and its complex, irrespective of light exposure. Show less

Organometallic complexes of the formula [Ru(N^N)(p-cymene)Cl][X] (N^N = bidentate polypyridyl ligands, p-cymene = 1-methyl-4-(1-methylethyl)-benzene, X = counter anion), are currently studied as possible candidates for the potential treatment of cancer. Searching for new organometallic compounds with good to moderate cytotoxic activities, a series of mononuclear water-soluble ruthenium(II)-arene complexes incorporating substituted pyridine-quinoline ligands, with pending -CH₂OH, -CO₂H and -CO₂Me groups in the 4-position of quinoline ring, were synthesized, for the first time, to study their possible effect to modulate the activity of the ruthenium p-cymene complexes. These include the [Ru(η⁶-p-cymene)(pqhyme)Cl][X] (X = Cl^- (1-Cl), PF₆^- (1-PF₆), pqhyme = 4-hydroxymethyl-2-(pyridin-2-yl)quinoline), [Ru(η⁶-p-cymene)(pqca)Cl][Cl] ((2-Cl), pqca = 4-carboxy-2-(pyridin-2-yl)quinoline), and [Ru(η⁶-p-cymene)(pqcame)Cl][X] (X = Cl^- (3-Cl), PF₆^- (3-PF₆), pqcame = 4-carboxymethyl-2-(pyridin-2-yl)quinoline) complexes, respectively. Identification of the complexes was based on multinuclear NMR and ATR-IR spectroscopic methods, elemental analysis, conductivity measurements, UV-Vis spectroscopic, and ESI-HRMS techniques. The solid-state structures of 1-PF₆ and 3-PF₆ have been elucidated by single-crystal X-ray diffraction revealing a three-legged piano stool geometry. This is the first time that the in vitro cytotoxic activities of these complexes are studied. These were conducted in HEK293T (human embryonic kidney cells) and HeLa cells (cervical cancer cells) via the MTT assay. The results show poor in vitro anticancer activities for the HeLa cancer cell lines and 3-Cl proved to be the most potent (IC₅₀ > 80 μΜ). In both cell lines, the cytotoxicity of the ligand precursor pqhyme is significantly higher than that of cisplatin. Show less

Treatment of malignant and non-malignant cultured human cell lines with a cytotoxic IC₅₀ dose of ∼2 μM tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(ii) chloride (RPC2) retards or arrests microtubule motion as tracked by visualizing fluorescently-tagged microtubule plus end-tracking proteins. Immunofluorescent microscopic images of the microtubules in fixed cells show substantial changes to cellular microtubule network and to overall cell morphology upon treatment with RPC2. Flow cytometry with MCF7 and H358 cells reveals only minor elevations of the number of cells in G₂/M phase, suggesting that the observed cytotoxicity is not tied to mitotic arrest. In vitro studies with purified tubulin reveal that RPC2 acts to promote tubulin polymerization and when imaged by electron microscopy, these microtubules look normal in appearance. Isothermal titration calorimetry measurements show an associative binding constant of 4.8 × 10⁶ M^-1 for RPC2 to preformed microtubules and support a 1 : 1 RPC2 to tubulin dimer stoichiometry. Competition experiments show RPC2 does not compete for the taxane binding site. Consistent with this tight binding, over 80% of the ruthenium in treated cells is co-localized with the cytoskeletal proteins. These data support RPC2 acting as an in vivo microtubule stabilizing agent and sharing many similarities with cells treated with paclitaxel. Show less

Two rhodium complexes Rh1 and Rh2 with isoquinoline derivatives were synthesized and characterized. Both complexes displayed strong anticancer activity against various cancer cells and low cytotoxicity against non-cancer cells. These complexes triggered apoptosis via mitochondrial dysfunction that increased the levels of ROS and Ca²⁺ and released cytochrome C which ultimately activated caspases and the apoptosis pathway. The different biological activities of Rh1 and Rh2 could be associated with the presence of methoxy substituents on the ligands. In vivo studies showed that Rh1 effectively inhibited tumor growth in a T-24 xenograft mouse model with a less adverse effect than cisplatin. Overall, Rh1 and Rh2 induced apoptosis via mitochondrial pathways and could be developed as effective anticancer agents. Show less

The in vitro cytotoxic properties of antimicrobial copper(II) complexes with 3,4,7,8-tetramethyl-1,10-phenanthroline (TMP) or 4,7-dipyridyl-1,10-phenanthroline (DIP) ligands and ruthenium(II) complexes coordinated with TMP or 2,9-dimethyl-1,10-phenanthroline ligands were investigated. Both copper(II) complexes were found to have similar inhibitory concentrations (IC₅₀~2-2.5μM). Their cytotoxicity was found to be necrotic, associated with cytoplasmic vacuolisation, rounding, detachment and lack of apoptosis-associated DNA fragmentation, in comparison to the apoptotic effects of cisplatin which demonstrate adherent cell enlargement or detachment, membrane blebbing and condensation. Antimicrobial ruthenium(II) complexes demonstrated a lower renal cytotoxicity than copper(II) complexes or cisplatin (IC₅₀>60μM). [Cu(DIP)(dach)](ClO₄)₂ and [Cu(TMP)(dach)](ClO₄)₂ (where dach=1,2-diaminocyclohexane) induced dihydroethidium-sensitive ROS and the cytotoxicity of both TMP and DIP coordinated copper(II) complexes was mitigated by catalase, highlighting a role of H₂O₂ generation in their mode of action. The cytotoxicity of either copper(II) complex was not affected by coincubation with organic cation transporter (OCT) inhibitors cimetidine or disopyramide, in contrast to cisplatin, suggesting a non-OCT dependent mode of uptake for the copper(II) complexes in human cells. Coincubation with copper sulfate reduced the cytotoxicity of [Cu(TMP)(dach)](ClO₄)₂ (3-6×). The TMP complex induced a greater degree of G2/M accumulation and micronuclei generation than the DIP complex, possibly attributable to its greater DNA binding affinity. These results highlight the potentially low genotoxicity of copper(II) complexes coordinated with TMP or DIP and polypyridyl ruthenium(II) complexes as potential antimicrobial agents. Show less

A set each of new bivalent and trivalent ruthenium complexes, [Ru(III)(HL)Cl2(EPh3)2] and [Ru(II)(L)(CO)(EPh3)2] (E = P (complexes and ) or As (complexes and )) were synthesised from the reactions of [Ru(III)Cl3(EPh3)3] with 2-hydroxynaphthaldehyde benzoic acid hydrazone (H2L) in methanol-chloroform and characterized by elemental analysis, spectral data and XRD study. A suitable mechanism to account for the formation of bivalent ruthenium carbonyl complexes from the corresponding trivalent precursors is provided by considering the role of added base in the reaction. Interaction of complexes with CT-DNA/bovine serum albumin was analysed with absorption and emission spectral titration studies. In vitro cytotoxic potential of the above ruthenium hydrazone complexes assayed against the A549 cell line revealed a significant growth inhibition. The test complexes added in IC50 concentration into the cell culture medium enhanced the release of lactate dehydrogenase, NO and reactive oxygen species in comparison with the control. Cell death induced by the complexes was studied using a propidium iodide staining assay and showed noticeable changes in the cell morphology which resembled apoptosis. Show less

A series of Ru(ii)(η(6)-p-cymene) complexes (1-4) bearing the general formula [RuCl2(η(6)-p-cymene)L] (L = monodentate aroylthiourea ligand) has been synthesized and characterized by analytical and various spectroscopic techniques. The neutral monodentate coordination of aroylthiourea with Ru via an S atom was confirmed by single crystal X-ray diffraction study. The complexes were tested for their ability to interact with DNA and protein. The complexes bound with calf thymus DNA (CT DNA) with the intrinsic binding constant value in the order of 10(4) M(-1). The intercalative mode of binding was confirmed by the ethidium bromide (EB) displacement study. The interaction of the complexes with CT DNA was further supported by viscosity measurements and circular dichroic (CD) spectra. The Ru(ii) complexes cleaved the supercoiled DNA without the need of any external agent. The spectroscopic evidence showed good binding efficacy of the complexes with BSA (Bovine Serum Albumin). The alterations in the secondary structure of BSA by the Ru(ii) complexes were confirmed by synchronous fluorescence spectra. Cytotoxicity examination by MTT assay was carried out in two cancer cell lines (MCF7 and A549) and one non-cancerous cell line (L929). Complex 4 showed significant activity [IC50 = 52.3 (MCF7) and 54.6 (A549) μM] which was comparable with that of similar known complexes. The morphological changes assessed by Hoechst staining revealed that the cell death occurred by apoptosis. Show less

Synthesis, spectral, electrochemical and single crystal X-ray diffraction data of a new series of DMSO containing bivalent ruthenium hydrazone complexes are presented. XRD data of two of the new complexes revealed an octahedral coordination around the ruthenium ion satisfied by NOS2Cl2 atoms. Electrochemical studies showed the metal centred, quasi-reversible, one-electron redox behaviour of the new complexes. The binding of these complexes with biomolecules such as calf thymus DNA (CT-DNA) and bovine serum albumin (BSA) protein investigated by different spectrophotometric methods revealed an intercalative mode of interaction. The in vitro cytotoxicity of these complexes evaluated by the MTT assay on a panel of cancer and normal cell lines indicated that the above complexes are more toxic to cancer cells with a few micromolar concentrations as the IC50 value, but are significantly less toxic to normal cell lines. The observed variations in the binding interactions and cytotoxicity of the complexes were attributed to the nature of the hydrazide moiety of the hydrazones that influences their biological activities. Show less

A new set of ruthenium(II) hydrazone complexes [Ru(H)(CO)(PPh3)2(L)] (1) and [RuCl2(DMSO)2(HL)] (2), with triphenyl phosphine or DMSO as co-ligands was synthesized by reacting benzoyl pyridine furoic acid hydrazone (HL) with [Ru(H)(Cl)(CO)(PPh3)3] and [RuCl2(DMSO)4]. The single crystal X-ray data of complexes 1 and 2 revealed an octahedral geometry around the ruthenium ion in which the hydrazone is coordinated through ON and NN atoms in complexes 1 and 2 respectively. The interaction of the compounds with calf thymus DNA (CT-DNA) has been estimated by absorption and emission titration methods which indicated that the ligand and the complexes interacted with CT-DNA through intercalation. In addition, the DNA cleavage ability of these newly synthesized ruthenium complexes assessed by an agarose gel electrophoresis method demonstrated that complex 2 has a higher DNA cleavage activity than that of complex 1. The binding properties of the free ligand and its complexes with bovine serum albumin (BSA) protein have been investigated using UV-visible, fluorescence and synchronous fluorescence spectroscopic methods which indicated the stronger binding nature of the ruthenium complexes to BSA than the free hydrazone ligand. Furthermore, the cytotoxicity of the compounds examined in vitro on a human cervical cancer cell line (HeLa) and a normal mouse embryonic fibroblasts cell line (NIH 3T3) revealed that complex 2 exhibited a superior cytotoxicity than complex 1 to the cancer cells but was less toxic to the normal mouse embryonic fibroblasts under identical conditions. Show less

Bivalent, ruthenium organometallics containing hydrazone ligands with the composition [RuH(CO)(PPh(3))(2)(L(1-3))] (4-6) have been synthesised from the reactions of [RuH(2)(CO)(PPh(3))(3)] and benzoic acid pyridine-2-ylmethylene-hydrazide (HL(1)) (1) /benzoic acid (1-pyridin-2-yl-ethylidene)-hydrazide (HL(2)) (2)/benzoic acid (phenyl-pyridin-2-yl-methylene)-hydrazide (HL(3)) (3) and characterised by various physico-chemical techniques. The X-ray crystal structure of one of the above complexes, [RuH(CO)(PPh(3))(2)(L(3))] (6) demonstrated a distorted octahedral coordination geometry around the metal centre. Results of our investigation on the effect of substitution (H or CH(3) or C(6)H(5)) at the azomethine carbon of coordinated hydrazone in these ruthenium chelates on the potential binding with DNA/BSA, free radical scavenging and cytotoxicity is presented. Show less